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LSC :a long read error correction tool
By Jit 2777 days agowww.healthcare.uiowa.edu - Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...Comparative genomics visualisation tools !
By Neel 1482 days agocmdcolin.github.io - Comparative genomics visualisation tools !Harvest: a suite of core-genome alignment and visualization tools
By Jit 3014 days agoharvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2847 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
Last updated 2988 days ago by Poonam Mahapatra Comments (1)BBSplit internally uses BBMap to map reads to multiple genomes at once, and determine which genome they match best. This is different than with ordinary mapping. If a genome (say, human) contains an exact repeat somewhere, reads mapping to it will...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 3013 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2772 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...Mulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 3155 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2882 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2825 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...
